1 /* 2 GAMG geometric-algebric multiogrid PC - Mark Adams 2011 3 */ 4 5 #include <../src/ksp/pc/impls/gamg/gamg.h> /*I "petscpc.h" I*/ 6 #include <petsc-private/kspimpl.h> 7 8 #if defined(PETSC_HAVE_TRIANGLE) 9 #define REAL PetscReal 10 #include <triangle.h> 11 #endif 12 13 #include <petscblaslapack.h> 14 15 /* Private context for the GAMG preconditioner */ 16 typedef struct { 17 PetscInt lid; /* local vertex index */ 18 PetscInt degree; /* vertex degree */ 19 } GAMGNode; 20 21 int petsc_geo_mg_compare(const void *a, const void *b) 22 { 23 return (((GAMGNode*)a)->degree - ((GAMGNode*)b)->degree); 24 } 25 26 /* -------------------------------------------------------------------------- */ 27 /* 28 PCSetCoordinates_GEO 29 30 Input Parameter: 31 . pc - the preconditioner context 32 */ 33 #undef __FUNCT__ 34 #define __FUNCT__ "PCSetCoordinates_GEO" 35 PetscErrorCode PCSetCoordinates_GEO(PC pc, PetscInt ndm, PetscInt a_nloc, PetscReal *coords) 36 { 37 PC_MG *mg = (PC_MG*)pc->data; 38 PC_GAMG *pc_gamg = (PC_GAMG*)mg->innerctx; 39 PetscErrorCode ierr; 40 PetscInt arrsz,bs,my0,kk,ii,nloc,Iend; 41 Mat Amat = pc->pmat; 42 43 PetscFunctionBegin; 44 PetscValidHeaderSpecific(Amat, MAT_CLASSID, 1); 45 ierr = MatGetBlockSize(Amat, &bs);CHKERRQ(ierr); 46 47 ierr = MatGetOwnershipRange(Amat, &my0, &Iend);CHKERRQ(ierr); 48 nloc = (Iend-my0)/bs; 49 50 if (nloc!=a_nloc) SETERRQ2(PetscObjectComm((PetscObject)Amat),PETSC_ERR_ARG_WRONG, "Stokes not supported nloc = %d %d.",a_nloc,nloc); 51 if ((Iend-my0)%bs!=0) SETERRQ1(PetscObjectComm((PetscObject)Amat),PETSC_ERR_ARG_WRONG, "Bad local size %d.",nloc); 52 53 pc_gamg->data_cell_rows = 1; 54 if (coords==0 && nloc > 0) SETERRQ(PetscObjectComm((PetscObject)Amat),PETSC_ERR_ARG_WRONG, "Need coordinates for pc_gamg_type 'geo'."); 55 pc_gamg->data_cell_cols = ndm; /* coordinates */ 56 57 arrsz = nloc*pc_gamg->data_cell_rows*pc_gamg->data_cell_cols; 58 59 /* create data - syntactic sugar that should be refactored at some point */ 60 if (pc_gamg->data==0 || (pc_gamg->data_sz != arrsz)) { 61 ierr = PetscFree(pc_gamg->data);CHKERRQ(ierr); 62 ierr = PetscMalloc1(arrsz+1, &pc_gamg->data);CHKERRQ(ierr); 63 } 64 for (kk=0; kk<arrsz; kk++) pc_gamg->data[kk] = -999.; 65 pc_gamg->data[arrsz] = -99.; 66 /* copy data in - column oriented */ 67 for (kk = 0; kk < nloc; kk++) { 68 for (ii = 0; ii < ndm; ii++) { 69 pc_gamg->data[ii*nloc + kk] = coords[kk*ndm + ii]; 70 } 71 } 72 if (pc_gamg->data[arrsz] != -99.) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"pc_gamg->data[arrsz %D] %g != -99.",arrsz,pc_gamg->data[arrsz]); 73 pc_gamg->data_sz = arrsz; 74 PetscFunctionReturn(0); 75 } 76 77 /* -------------------------------------------------------------------------- */ 78 /* 79 PCSetData_GEO 80 81 Input Parameter: 82 . pc - 83 */ 84 #undef __FUNCT__ 85 #define __FUNCT__ "PCSetData_GEO" 86 PetscErrorCode PCSetData_GEO(PC pc, Mat m) 87 { 88 PetscFunctionBegin; 89 SETERRQ(PetscObjectComm((PetscObject)pc),PETSC_ERR_PLIB,"GEO MG needs coordinates"); 90 } 91 92 /* -------------------------------------------------------------------------- */ 93 /* 94 PCSetFromOptions_GEO 95 96 Input Parameter: 97 . pc - 98 */ 99 #undef __FUNCT__ 100 #define __FUNCT__ "PCSetFromOptions_GEO" 101 PetscErrorCode PCSetFromOptions_GEO(PetscOptions *PetscOptionsObject,PC pc) 102 { 103 PetscErrorCode ierr; 104 105 PetscFunctionBegin; 106 ierr = PetscOptionsHead(PetscOptionsObject,"GAMG-GEO options");CHKERRQ(ierr); 107 { 108 /* -pc_gamg_sa_nsmooths */ 109 /* pc_gamg_sa->smooths = 0; */ 110 /* ierr = PetscOptionsInt("-pc_gamg_agg_nsmooths", */ 111 /* "smoothing steps for smoothed aggregation, usually 1 (0)", */ 112 /* "PCGAMGSetNSmooths_AGG", */ 113 /* pc_gamg_sa->smooths, */ 114 /* &pc_gamg_sa->smooths, */ 115 /* &flag); */ 116 /* CHKERRQ(ierr); */ 117 } 118 ierr = PetscOptionsTail();CHKERRQ(ierr); 119 PetscFunctionReturn(0); 120 } 121 122 /* -------------------------------------------------------------------------- */ 123 /* 124 triangulateAndFormProl 125 126 Input Parameter: 127 . selected_2 - list of selected local ID, includes selected ghosts 128 . data_stride - 129 . coords[2*data_stride] - column vector of local coordinates w/ ghosts 130 . nselected_1 - selected IDs that go with base (1) graph 131 . clid_lid_1[nselected_1] - lids of selected (c) nodes ??????????? 132 . agg_lists_1 - list of aggregates 133 . crsGID[selected.size()] - global index for prolongation operator 134 . bs - block size 135 Output Parameter: 136 . a_Prol - prolongation operator 137 . a_worst_best - measure of worst missed fine vertex, 0 is no misses 138 */ 139 #undef __FUNCT__ 140 #define __FUNCT__ "triangulateAndFormProl" 141 static PetscErrorCode triangulateAndFormProl(IS selected_2, /* list of selected local ID, includes selected ghosts */ 142 const PetscInt data_stride, 143 const PetscReal coords[], /* column vector of local coordinates w/ ghosts */ 144 const PetscInt nselected_1, /* list of selected local ID, includes selected ghosts */ 145 const PetscInt clid_lid_1[], 146 const PetscCoarsenData *agg_lists_1, /* selected_1 vertices of aggregate unselected vertices */ 147 const PetscInt crsGID[], 148 const PetscInt bs, 149 Mat a_Prol, /* prolongation operator (output) */ 150 PetscReal *a_worst_best) /* measure of worst missed fine vertex, 0 is no misses */ 151 { 152 #if defined(PETSC_HAVE_TRIANGLE) 153 PetscErrorCode ierr; 154 PetscInt jj,tid,tt,idx,nselected_2; 155 struct triangulateio in,mid; 156 const PetscInt *selected_idx_2; 157 PetscMPIInt rank; 158 PetscInt Istart,Iend,nFineLoc,myFine0; 159 int kk,nPlotPts,sid; 160 MPI_Comm comm; 161 PetscReal tm; 162 163 PetscFunctionBegin; 164 ierr = PetscObjectGetComm((PetscObject)a_Prol,&comm);CHKERRQ(ierr); 165 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 166 ierr = ISGetSize(selected_2, &nselected_2);CHKERRQ(ierr); 167 if (nselected_2 == 1 || nselected_2 == 2) { /* 0 happens on idle processors */ 168 *a_worst_best = 100.0; /* this will cause a stop, but not globalized (should not happen) */ 169 } else *a_worst_best = 0.0; 170 ierr = MPI_Allreduce(a_worst_best, &tm, 1, MPIU_REAL, MPIU_MAX, comm);CHKERRQ(ierr); 171 if (tm > 0.0) { 172 *a_worst_best = 100.0; 173 PetscFunctionReturn(0); 174 } 175 ierr = MatGetOwnershipRange(a_Prol, &Istart, &Iend);CHKERRQ(ierr); 176 nFineLoc = (Iend-Istart)/bs; myFine0 = Istart/bs; 177 nPlotPts = nFineLoc; /* locals */ 178 /* traingle */ 179 /* Define input points - in*/ 180 in.numberofpoints = nselected_2; 181 in.numberofpointattributes = 0; 182 /* get nselected points */ 183 ierr = PetscMalloc1(2*(nselected_2), &in.pointlist);CHKERRQ(ierr); 184 ierr = ISGetIndices(selected_2, &selected_idx_2);CHKERRQ(ierr); 185 186 for (kk=0,sid=0; kk<nselected_2; kk++,sid += 2) { 187 PetscInt lid = selected_idx_2[kk]; 188 in.pointlist[sid] = coords[lid]; 189 in.pointlist[sid+1] = coords[data_stride + lid]; 190 if (lid>=nFineLoc) nPlotPts++; 191 } 192 if (sid != 2*nselected_2) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"sid %D != 2*nselected_2 %D",sid,nselected_2); 193 194 in.numberofsegments = 0; 195 in.numberofedges = 0; 196 in.numberofholes = 0; 197 in.numberofregions = 0; 198 in.trianglelist = 0; 199 in.segmentmarkerlist = 0; 200 in.pointattributelist = 0; 201 in.pointmarkerlist = 0; 202 in.triangleattributelist = 0; 203 in.trianglearealist = 0; 204 in.segmentlist = 0; 205 in.holelist = 0; 206 in.regionlist = 0; 207 in.edgelist = 0; 208 in.edgemarkerlist = 0; 209 in.normlist = 0; 210 211 /* triangulate */ 212 mid.pointlist = 0; /* Not needed if -N switch used. */ 213 /* Not needed if -N switch used or number of point attributes is zero: */ 214 mid.pointattributelist = 0; 215 mid.pointmarkerlist = 0; /* Not needed if -N or -B switch used. */ 216 mid.trianglelist = 0; /* Not needed if -E switch used. */ 217 /* Not needed if -E switch used or number of triangle attributes is zero: */ 218 mid.triangleattributelist = 0; 219 mid.neighborlist = 0; /* Needed only if -n switch used. */ 220 /* Needed only if segments are output (-p or -c) and -P not used: */ 221 mid.segmentlist = 0; 222 /* Needed only if segments are output (-p or -c) and -P and -B not used: */ 223 mid.segmentmarkerlist = 0; 224 mid.edgelist = 0; /* Needed only if -e switch used. */ 225 mid.edgemarkerlist = 0; /* Needed if -e used and -B not used. */ 226 mid.numberoftriangles = 0; 227 228 /* Triangulate the points. Switches are chosen to read and write a */ 229 /* PSLG (p), preserve the convex hull (c), number everything from */ 230 /* zero (z), assign a regional attribute to each element (A), and */ 231 /* produce an edge list (e), a Voronoi diagram (v), and a triangle */ 232 /* neighbor list (n). */ 233 if (nselected_2 != 0) { /* inactive processor */ 234 char args[] = "npczQ"; /* c is needed ? */ 235 triangulate(args, &in, &mid, (struct triangulateio*) NULL); 236 /* output .poly files for 'showme' */ 237 if (!PETSC_TRUE) { 238 static int level = 1; 239 FILE *file; char fname[32]; 240 241 sprintf(fname,"C%d_%d.poly",level,rank); file = fopen(fname, "w"); 242 /*First line: <# of vertices> <dimension (must be 2)> <# of attributes> <# of boundary markers (0 or 1)>*/ 243 fprintf(file, "%d %d %d %d\n",in.numberofpoints,2,0,0); 244 /*Following lines: <vertex #> <x> <y> */ 245 for (kk=0,sid=0; kk<in.numberofpoints; kk++,sid += 2) { 246 fprintf(file, "%d %e %e\n",kk,in.pointlist[sid],in.pointlist[sid+1]); 247 } 248 /*One line: <# of segments> <# of boundary markers (0 or 1)> */ 249 fprintf(file, "%d %d\n",0,0); 250 /*Following lines: <segment #> <endpoint> <endpoint> [boundary marker] */ 251 /* One line: <# of holes> */ 252 fprintf(file, "%d\n",0); 253 /* Following lines: <hole #> <x> <y> */ 254 /* Optional line: <# of regional attributes and/or area constraints> */ 255 /* Optional following lines: <region #> <x> <y> <attribute> <maximum area> */ 256 fclose(file); 257 258 /* elems */ 259 sprintf(fname,"C%d_%d.ele",level,rank); file = fopen(fname, "w"); 260 /* First line: <# of triangles> <nodes per triangle> <# of attributes> */ 261 fprintf(file, "%d %d %d\n",mid.numberoftriangles,3,0); 262 /* Remaining lines: <triangle #> <node> <node> <node> ... [attributes] */ 263 for (kk=0,sid=0; kk<mid.numberoftriangles; kk++,sid += 3) { 264 fprintf(file, "%d %d %d %d\n",kk,mid.trianglelist[sid],mid.trianglelist[sid+1],mid.trianglelist[sid+2]); 265 } 266 fclose(file); 267 268 sprintf(fname,"C%d_%d.node",level,rank); file = fopen(fname, "w"); 269 /* First line: <# of vertices> <dimension (must be 2)> <# of attributes> <# of boundary markers (0 or 1)> */ 270 /* fprintf(file, "%d %d %d %d\n",in.numberofpoints,2,0,0); */ 271 fprintf(file, "%d %d %d %d\n",nPlotPts,2,0,0); 272 /*Following lines: <vertex #> <x> <y> */ 273 for (kk=0,sid=0; kk<in.numberofpoints; kk++,sid+=2) { 274 fprintf(file, "%d %e %e\n",kk,in.pointlist[sid],in.pointlist[sid+1]); 275 } 276 277 sid /= 2; 278 for (jj=0; jj<nFineLoc; jj++) { 279 PetscBool sel = PETSC_TRUE; 280 for (kk=0; kk<nselected_2 && sel; kk++) { 281 PetscInt lid = selected_idx_2[kk]; 282 if (lid == jj) sel = PETSC_FALSE; 283 } 284 if (sel) fprintf(file, "%d %e %e\n",sid++,coords[jj],coords[data_stride + jj]); 285 } 286 fclose(file); 287 if (sid != nPlotPts) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"sid %D != nPlotPts %D",sid,nPlotPts); 288 level++; 289 } 290 } 291 #if defined PETSC_GAMG_USE_LOG 292 ierr = PetscLogEventBegin(petsc_gamg_setup_events[FIND_V],0,0,0,0);CHKERRQ(ierr); 293 #endif 294 { /* form P - setup some maps */ 295 PetscInt clid,mm,*nTri,*node_tri; 296 297 ierr = PetscMalloc1(nselected_2, &node_tri);CHKERRQ(ierr); 298 ierr = PetscMalloc1(nselected_2, &nTri);CHKERRQ(ierr); 299 300 /* need list of triangles on node */ 301 for (kk=0; kk<nselected_2; kk++) nTri[kk] = 0; 302 for (tid=0,kk=0; tid<mid.numberoftriangles; tid++) { 303 for (jj=0; jj<3; jj++) { 304 PetscInt cid = mid.trianglelist[kk++]; 305 if (nTri[cid] == 0) node_tri[cid] = tid; 306 nTri[cid]++; 307 } 308 } 309 #define EPS 1.e-12 310 /* find points and set prolongation */ 311 for (mm = clid = 0; mm < nFineLoc; mm++) { 312 PetscBool ise; 313 ierr = PetscCDEmptyAt(agg_lists_1,mm,&ise);CHKERRQ(ierr); 314 if (!ise) { 315 const PetscInt lid = mm; 316 /* for (clid_iterator=0;clid_iterator<nselected_1;clid_iterator++) { */ 317 PetscScalar AA[3][3]; 318 PetscBLASInt N=3,NRHS=1,LDA=3,IPIV[3],LDB=3,INFO; 319 PetscCDPos pos; 320 ierr = PetscCDGetHeadPos(agg_lists_1,lid,&pos);CHKERRQ(ierr); 321 while (pos) { 322 PetscInt flid; 323 ierr = PetscLLNGetID(pos, &flid);CHKERRQ(ierr); 324 ierr = PetscCDGetNextPos(agg_lists_1,lid,&pos);CHKERRQ(ierr); 325 326 if (flid < nFineLoc) { /* could be a ghost */ 327 PetscInt bestTID = -1; PetscReal best_alpha = 1.e10; 328 const PetscInt fgid = flid + myFine0; 329 /* compute shape function for gid */ 330 const PetscReal fcoord[3] = {coords[flid],coords[data_stride+flid],1.0}; 331 PetscBool haveit =PETSC_FALSE; PetscScalar alpha[3]; PetscInt clids[3]; 332 333 /* look for it */ 334 for (tid = node_tri[clid], jj=0; 335 jj < 5 && !haveit && tid != -1; 336 jj++) { 337 for (tt=0; tt<3; tt++) { 338 PetscInt cid2 = mid.trianglelist[3*tid + tt]; 339 PetscInt lid2 = selected_idx_2[cid2]; 340 AA[tt][0] = coords[lid2]; AA[tt][1] = coords[data_stride + lid2]; AA[tt][2] = 1.0; 341 clids[tt] = cid2; /* store for interp */ 342 } 343 344 for (tt=0; tt<3; tt++) alpha[tt] = (PetscScalar)fcoord[tt]; 345 346 /* SUBROUTINE DGESV(N, NRHS, A, LDA, IPIV, B, LDB, INFO) */ 347 PetscStackCallBLAS("LAPACKgesv",LAPACKgesv_(&N, &NRHS, (PetscScalar*)AA, &LDA, IPIV, alpha, &LDB, &INFO)); 348 { 349 PetscBool have=PETSC_TRUE; PetscReal lowest=1.e10; 350 for (tt = 0, idx = 0; tt < 3; tt++) { 351 if (PetscRealPart(alpha[tt]) > (1.0+EPS) || PetscRealPart(alpha[tt]) < -EPS) have = PETSC_FALSE; 352 if (PetscRealPart(alpha[tt]) < lowest) { 353 lowest = PetscRealPart(alpha[tt]); 354 idx = tt; 355 } 356 } 357 haveit = have; 358 } 359 tid = mid.neighborlist[3*tid + idx]; 360 } 361 362 if (!haveit) { 363 /* brute force */ 364 for (tid=0; tid<mid.numberoftriangles && !haveit; tid++) { 365 for (tt=0; tt<3; tt++) { 366 PetscInt cid2 = mid.trianglelist[3*tid + tt]; 367 PetscInt lid2 = selected_idx_2[cid2]; 368 AA[tt][0] = coords[lid2]; AA[tt][1] = coords[data_stride + lid2]; AA[tt][2] = 1.0; 369 clids[tt] = cid2; /* store for interp */ 370 } 371 for (tt=0; tt<3; tt++) alpha[tt] = fcoord[tt]; 372 /* SUBROUTINE DGESV(N, NRHS, A, LDA, IPIV, B, LDB, INFO) */ 373 PetscStackCallBLAS("LAPACKgesv",LAPACKgesv_(&N, &NRHS, (PetscScalar*)AA, &LDA, IPIV, alpha, &LDB, &INFO)); 374 { 375 PetscBool have=PETSC_TRUE; PetscReal worst=0.0, v; 376 for (tt=0; tt<3 && have; tt++) { 377 if (PetscRealPart(alpha[tt]) > 1.0+EPS || PetscRealPart(alpha[tt]) < -EPS) have=PETSC_FALSE; 378 if ((v=PetscAbs(PetscRealPart(alpha[tt])-0.5)) > worst) worst = v; 379 } 380 if (worst < best_alpha) { 381 best_alpha = worst; bestTID = tid; 382 } 383 haveit = have; 384 } 385 } 386 } 387 if (!haveit) { 388 if (best_alpha > *a_worst_best) *a_worst_best = best_alpha; 389 /* use best one */ 390 for (tt=0; tt<3; tt++) { 391 PetscInt cid2 = mid.trianglelist[3*bestTID + tt]; 392 PetscInt lid2 = selected_idx_2[cid2]; 393 AA[tt][0] = coords[lid2]; AA[tt][1] = coords[data_stride + lid2]; AA[tt][2] = 1.0; 394 clids[tt] = cid2; /* store for interp */ 395 } 396 for (tt=0; tt<3; tt++) alpha[tt] = fcoord[tt]; 397 /* SUBROUTINE DGESV(N, NRHS, A, LDA, IPIV, B, LDB, INFO) */ 398 PetscStackCallBLAS("LAPACKgesv",LAPACKgesv_(&N, &NRHS, (PetscScalar*)AA, &LDA, IPIV, alpha, &LDB, &INFO)); 399 } 400 401 /* put in row of P */ 402 for (idx=0; idx<3; idx++) { 403 PetscScalar shp = alpha[idx]; 404 if (PetscAbs(PetscRealPart(shp)) > 1.e-6) { 405 PetscInt cgid = crsGID[clids[idx]]; 406 PetscInt jj = cgid*bs, ii = fgid*bs; /* need to gloalize */ 407 for (tt=0; tt < bs; tt++, ii++, jj++) { 408 ierr = MatSetValues(a_Prol,1,&ii,1,&jj,&shp,INSERT_VALUES);CHKERRQ(ierr); 409 } 410 } 411 } 412 } 413 } /* aggregates iterations */ 414 clid++; 415 } /* a coarse agg */ 416 } /* for all fine nodes */ 417 418 ierr = ISRestoreIndices(selected_2, &selected_idx_2);CHKERRQ(ierr); 419 ierr = MatAssemblyBegin(a_Prol,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 420 ierr = MatAssemblyEnd(a_Prol,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 421 422 ierr = PetscFree(node_tri);CHKERRQ(ierr); 423 ierr = PetscFree(nTri);CHKERRQ(ierr); 424 } 425 #if defined PETSC_GAMG_USE_LOG 426 ierr = PetscLogEventEnd(petsc_gamg_setup_events[FIND_V],0,0,0,0);CHKERRQ(ierr); 427 #endif 428 free(mid.trianglelist); 429 free(mid.neighborlist); 430 ierr = PetscFree(in.pointlist);CHKERRQ(ierr); 431 PetscFunctionReturn(0); 432 #else 433 SETERRQ(PetscObjectComm((PetscObject)a_Prol),PETSC_ERR_PLIB,"configure with TRIANGLE to use geometric MG"); 434 #endif 435 } 436 /* -------------------------------------------------------------------------- */ 437 /* 438 getGIDsOnSquareGraph - square graph, get 439 440 Input Parameter: 441 . nselected_1 - selected local indices (includes ghosts in input Gmat1) 442 . clid_lid_1 - [nselected_1] lids of selected nodes 443 . Gmat1 - graph that goes with 'selected_1' 444 Output Parameter: 445 . a_selected_2 - selected local indices (includes ghosts in output a_Gmat_2) 446 . a_Gmat_2 - graph that is squared of 'Gmat_1' 447 . a_crsGID[a_selected_2.size()] - map of global IDs of coarse grid nodes 448 */ 449 #undef __FUNCT__ 450 #define __FUNCT__ "getGIDsOnSquareGraph" 451 static PetscErrorCode getGIDsOnSquareGraph(const PetscInt nselected_1,const PetscInt clid_lid_1[],const Mat Gmat1,IS *a_selected_2,Mat *a_Gmat_2,PetscInt **a_crsGID) 452 { 453 PetscErrorCode ierr; 454 PetscMPIInt size; 455 PetscInt *crsGID, kk,my0,Iend,nloc; 456 MPI_Comm comm; 457 458 PetscFunctionBegin; 459 ierr = PetscObjectGetComm((PetscObject)Gmat1,&comm);CHKERRQ(ierr); 460 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 461 ierr = MatGetOwnershipRange(Gmat1,&my0,&Iend);CHKERRQ(ierr); /* AIJ */ 462 nloc = Iend - my0; /* this does not change */ 463 464 if (size == 1) { /* not much to do in serial */ 465 ierr = PetscMalloc1(nselected_1, &crsGID);CHKERRQ(ierr); 466 for (kk=0; kk<nselected_1; kk++) crsGID[kk] = kk; 467 *a_Gmat_2 = 0; 468 ierr = ISCreateGeneral(PETSC_COMM_SELF,nselected_1,clid_lid_1,PETSC_COPY_VALUES,a_selected_2);CHKERRQ(ierr); 469 } else { 470 PetscInt idx,num_fine_ghosts,num_crs_ghost,myCrs0; 471 Mat_MPIAIJ *mpimat2; 472 Mat Gmat2; 473 Vec locState; 474 PetscScalar *cpcol_state; 475 476 /* scan my coarse zero gid, set 'lid_state' with coarse GID */ 477 kk = nselected_1; 478 MPI_Scan(&kk, &myCrs0, 1, MPIU_INT, MPIU_SUM, comm); 479 myCrs0 -= nselected_1; 480 481 if (a_Gmat_2) { /* output */ 482 /* grow graph to get wider set of selected vertices to cover fine grid, invalidates 'llist' */ 483 ierr = MatTransposeMatMult(Gmat1, Gmat1, MAT_INITIAL_MATRIX, PETSC_DEFAULT, &Gmat2);CHKERRQ(ierr); 484 *a_Gmat_2 = Gmat2; /* output */ 485 } else Gmat2 = Gmat1; /* use local to get crsGIDs at least */ 486 /* get coarse grid GIDS for selected (locals and ghosts) */ 487 mpimat2 = (Mat_MPIAIJ*)Gmat2->data; 488 ierr = MatCreateVecs(Gmat2, &locState, 0);CHKERRQ(ierr); 489 ierr = VecSet(locState, (PetscScalar)(PetscReal)(-1));CHKERRQ(ierr); /* set with UNKNOWN state */ 490 for (kk=0; kk<nselected_1; kk++) { 491 PetscInt fgid = clid_lid_1[kk] + my0; 492 PetscScalar v = (PetscScalar)(kk+myCrs0); 493 ierr = VecSetValues(locState, 1, &fgid, &v, INSERT_VALUES);CHKERRQ(ierr); /* set with PID */ 494 } 495 ierr = VecAssemblyBegin(locState);CHKERRQ(ierr); 496 ierr = VecAssemblyEnd(locState);CHKERRQ(ierr); 497 ierr = VecScatterBegin(mpimat2->Mvctx,locState,mpimat2->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 498 ierr = VecScatterEnd(mpimat2->Mvctx,locState,mpimat2->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 499 ierr = VecGetLocalSize(mpimat2->lvec, &num_fine_ghosts);CHKERRQ(ierr); 500 ierr = VecGetArray(mpimat2->lvec, &cpcol_state);CHKERRQ(ierr); 501 for (kk=0,num_crs_ghost=0; kk<num_fine_ghosts; kk++) { 502 if ((PetscInt)PetscRealPart(cpcol_state[kk]) != -1) num_crs_ghost++; 503 } 504 ierr = PetscMalloc1(nselected_1+num_crs_ghost, &crsGID);CHKERRQ(ierr); /* output */ 505 { 506 PetscInt *selected_set; 507 ierr = PetscMalloc1(nselected_1+num_crs_ghost, &selected_set);CHKERRQ(ierr); 508 /* do ghost of 'crsGID' */ 509 for (kk=0,idx=nselected_1; kk<num_fine_ghosts; kk++) { 510 if ((PetscInt)PetscRealPart(cpcol_state[kk]) != -1) { 511 PetscInt cgid = (PetscInt)PetscRealPart(cpcol_state[kk]); 512 selected_set[idx] = nloc + kk; 513 crsGID[idx++] = cgid; 514 } 515 } 516 if (idx != (nselected_1+num_crs_ghost)) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_PLIB,"idx %D != (nselected_1 %D + num_crs_ghost %D)",idx,nselected_1,num_crs_ghost); 517 ierr = VecRestoreArray(mpimat2->lvec, &cpcol_state);CHKERRQ(ierr); 518 /* do locals in 'crsGID' */ 519 ierr = VecGetArray(locState, &cpcol_state);CHKERRQ(ierr); 520 for (kk=0,idx=0; kk<nloc; kk++) { 521 if ((PetscInt)PetscRealPart(cpcol_state[kk]) != -1) { 522 PetscInt cgid = (PetscInt)PetscRealPart(cpcol_state[kk]); 523 selected_set[idx] = kk; 524 crsGID[idx++] = cgid; 525 } 526 } 527 if (idx != nselected_1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"idx %D != nselected_1 %D",idx,nselected_1); 528 ierr = VecRestoreArray(locState, &cpcol_state);CHKERRQ(ierr); 529 530 if (a_selected_2 != 0) { /* output */ 531 ierr = ISCreateGeneral(PETSC_COMM_SELF,(nselected_1+num_crs_ghost),selected_set,PETSC_OWN_POINTER,a_selected_2);CHKERRQ(ierr); 532 } else { 533 ierr = PetscFree(selected_set);CHKERRQ(ierr); 534 } 535 } 536 ierr = VecDestroy(&locState);CHKERRQ(ierr); 537 } 538 *a_crsGID = crsGID; /* output */ 539 PetscFunctionReturn(0); 540 } 541 542 /* -------------------------------------------------------------------------- */ 543 /* 544 PCGAMGGraph_GEO 545 546 Input Parameter: 547 . pc - this 548 . Amat - matrix on this fine level 549 Output Parameter: 550 . a_Gmat 551 */ 552 #undef __FUNCT__ 553 #define __FUNCT__ "PCGAMGGraph_GEO" 554 PetscErrorCode PCGAMGGraph_GEO(PC pc,const Mat Amat,Mat *a_Gmat) 555 { 556 PetscErrorCode ierr; 557 PC_MG *mg = (PC_MG*)pc->data; 558 PC_GAMG *pc_gamg = (PC_GAMG*)mg->innerctx; 559 const PetscReal vfilter = pc_gamg->threshold; 560 MPI_Comm comm; 561 Mat Gmat; 562 PetscBool set,flg,symm; 563 564 PetscFunctionBegin; 565 ierr = PetscObjectGetComm((PetscObject)Amat,&comm);CHKERRQ(ierr); 566 ierr = PetscLogEventBegin(PC_GAMGGraph_GEO,0,0,0,0);CHKERRQ(ierr); 567 568 ierr = MatIsSymmetricKnown(Amat, &set, &flg);CHKERRQ(ierr); 569 symm = (PetscBool)!(set && flg); 570 571 ierr = PCGAMGCreateGraph(Amat, &Gmat);CHKERRQ(ierr); 572 ierr = PCGAMGFilterGraph(&Gmat, vfilter, symm);CHKERRQ(ierr); 573 574 *a_Gmat = Gmat; 575 ierr = PetscLogEventEnd(PC_GAMGGraph_GEO,0,0,0,0);CHKERRQ(ierr); 576 PetscFunctionReturn(0); 577 } 578 579 /* -------------------------------------------------------------------------- */ 580 /* 581 PCGAMGCoarsen_GEO 582 583 Input Parameter: 584 . a_pc - this 585 . a_Gmat - graph 586 Output Parameter: 587 . a_llist_parent - linked list from selected indices for data locality only 588 */ 589 #undef __FUNCT__ 590 #define __FUNCT__ "PCGAMGCoarsen_GEO" 591 PetscErrorCode PCGAMGCoarsen_GEO(PC a_pc,Mat *a_Gmat,PetscCoarsenData **a_llist_parent) 592 { 593 PetscErrorCode ierr; 594 PC_MG *mg = (PC_MG*)a_pc->data; 595 PetscInt Istart,Iend,nloc,kk,Ii,ncols; 596 IS perm; 597 GAMGNode *gnodes; 598 PetscInt *permute; 599 Mat Gmat = *a_Gmat; 600 MPI_Comm comm; 601 MatCoarsen crs; 602 603 PetscFunctionBegin; 604 ierr = PetscObjectGetComm((PetscObject)a_pc,&comm);CHKERRQ(ierr); 605 ierr = PetscLogEventBegin(PC_GAMGCoarsen_GEO,0,0,0,0);CHKERRQ(ierr); 606 ierr = MatGetOwnershipRange(Gmat, &Istart, &Iend);CHKERRQ(ierr); 607 nloc = (Iend-Istart); 608 609 /* create random permutation with sort for geo-mg */ 610 ierr = PetscMalloc1(nloc, &gnodes);CHKERRQ(ierr); 611 ierr = PetscMalloc1(nloc, &permute);CHKERRQ(ierr); 612 613 for (Ii=Istart; Ii<Iend; Ii++) { /* locals only? */ 614 ierr = MatGetRow(Gmat,Ii,&ncols,0,0);CHKERRQ(ierr); 615 { 616 PetscInt lid = Ii - Istart; 617 gnodes[lid].lid = lid; 618 gnodes[lid].degree = ncols; 619 } 620 ierr = MatRestoreRow(Gmat,Ii,&ncols,0,0);CHKERRQ(ierr); 621 } 622 /* randomize */ 623 srand(1); /* make deterministic */ 624 if (PETSC_TRUE) { 625 PetscBool *bIndexSet; 626 ierr = PetscMalloc1(nloc, &bIndexSet);CHKERRQ(ierr); 627 for (Ii = 0; Ii < nloc; Ii++) bIndexSet[Ii] = PETSC_FALSE; 628 for (Ii = 0; Ii < nloc; Ii++) { 629 PetscInt iSwapIndex = rand()%nloc; 630 if (!bIndexSet[iSwapIndex] && iSwapIndex != Ii) { 631 GAMGNode iTemp = gnodes[iSwapIndex]; 632 gnodes[iSwapIndex] = gnodes[Ii]; 633 gnodes[Ii] = iTemp; 634 bIndexSet[Ii] = PETSC_TRUE; 635 bIndexSet[iSwapIndex] = PETSC_TRUE; 636 } 637 } 638 ierr = PetscFree(bIndexSet);CHKERRQ(ierr); 639 } 640 /* only sort locals */ 641 qsort(gnodes, nloc, sizeof(GAMGNode), petsc_geo_mg_compare); 642 /* create IS of permutation */ 643 for (kk=0; kk<nloc; kk++) permute[kk] = gnodes[kk].lid; /* locals only */ 644 ierr = ISCreateGeneral(PETSC_COMM_SELF, nloc, permute, PETSC_OWN_POINTER, &perm);CHKERRQ(ierr); 645 646 ierr = PetscFree(gnodes);CHKERRQ(ierr); 647 648 /* get MIS aggs */ 649 650 ierr = MatCoarsenCreate(comm, &crs);CHKERRQ(ierr); 651 ierr = MatCoarsenSetType(crs, MATCOARSENMIS);CHKERRQ(ierr); 652 ierr = MatCoarsenSetGreedyOrdering(crs, perm);CHKERRQ(ierr); 653 ierr = MatCoarsenSetAdjacency(crs, Gmat);CHKERRQ(ierr); 654 ierr = MatCoarsenSetStrictAggs(crs, PETSC_FALSE);CHKERRQ(ierr); 655 ierr = MatCoarsenApply(crs);CHKERRQ(ierr); 656 ierr = MatCoarsenGetData(crs, a_llist_parent);CHKERRQ(ierr); 657 ierr = MatCoarsenDestroy(&crs);CHKERRQ(ierr); 658 659 ierr = ISDestroy(&perm);CHKERRQ(ierr); 660 ierr = PetscLogEventEnd(PC_GAMGCoarsen_GEO,0,0,0,0);CHKERRQ(ierr); 661 PetscFunctionReturn(0); 662 } 663 664 /* -------------------------------------------------------------------------- */ 665 /* 666 PCGAMGProlongator_GEO 667 668 Input Parameter: 669 . pc - this 670 . Amat - matrix on this fine level 671 . Graph - used to get ghost data for nodes in 672 . selected_1 - [nselected] 673 . agg_lists - [nselected] 674 Output Parameter: 675 . a_P_out - prolongation operator to the next level 676 */ 677 #undef __FUNCT__ 678 #define __FUNCT__ "PCGAMGProlongator_GEO" 679 PetscErrorCode PCGAMGProlongator_GEO(PC pc,const Mat Amat,const Mat Gmat,PetscCoarsenData *agg_lists,Mat *a_P_out) 680 { 681 PC_MG *mg = (PC_MG*)pc->data; 682 PC_GAMG *pc_gamg = (PC_GAMG*)mg->innerctx; 683 const PetscInt dim = pc_gamg->data_cell_cols, data_cols = pc_gamg->data_cell_cols; 684 PetscErrorCode ierr; 685 PetscInt Istart,Iend,nloc,my0,jj,kk,ncols,nLocalSelected,bs,*clid_flid; 686 Mat Prol; 687 PetscMPIInt rank, size; 688 MPI_Comm comm; 689 IS selected_2,selected_1; 690 const PetscInt *selected_idx; 691 692 PetscFunctionBegin; 693 ierr = PetscObjectGetComm((PetscObject)Amat,&comm);CHKERRQ(ierr); 694 ierr = PetscLogEventBegin(PC_GAMGProlongator_GEO,0,0,0,0);CHKERRQ(ierr); 695 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 696 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 697 ierr = MatGetOwnershipRange(Amat, &Istart, &Iend);CHKERRQ(ierr); 698 ierr = MatGetBlockSize(Amat, &bs);CHKERRQ(ierr); 699 nloc = (Iend-Istart)/bs; my0 = Istart/bs; 700 if ((Iend-Istart) % bs) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_PLIB,"(Iend %D - Istart %D) % bs %D",Iend,Istart,bs); 701 702 /* get 'nLocalSelected' */ 703 ierr = PetscCDGetMIS(agg_lists, &selected_1);CHKERRQ(ierr); 704 ierr = ISGetSize(selected_1, &jj);CHKERRQ(ierr); 705 ierr = PetscMalloc1(jj, &clid_flid);CHKERRQ(ierr); 706 ierr = ISGetIndices(selected_1, &selected_idx);CHKERRQ(ierr); 707 for (kk=0,nLocalSelected=0; kk<jj; kk++) { 708 PetscInt lid = selected_idx[kk]; 709 if (lid<nloc) { 710 ierr = MatGetRow(Gmat,lid+my0,&ncols,0,0);CHKERRQ(ierr); 711 if (ncols>1) clid_flid[nLocalSelected++] = lid; /* fiter out singletons */ 712 ierr = MatRestoreRow(Gmat,lid+my0,&ncols,0,0);CHKERRQ(ierr); 713 } 714 } 715 ierr = ISRestoreIndices(selected_1, &selected_idx);CHKERRQ(ierr); 716 ierr = ISDestroy(&selected_1);CHKERRQ(ierr); /* this is selected_1 in serial */ 717 718 /* create prolongator, create P matrix */ 719 ierr = MatCreate(comm, &Prol);CHKERRQ(ierr); 720 ierr = MatSetSizes(Prol,nloc*bs,nLocalSelected*bs,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 721 ierr = MatSetBlockSizes(Prol, bs, bs);CHKERRQ(ierr); 722 ierr = MatSetType(Prol, MATAIJ);CHKERRQ(ierr); 723 ierr = MatSeqAIJSetPreallocation(Prol,3*data_cols,NULL);CHKERRQ(ierr); 724 ierr = MatMPIAIJSetPreallocation(Prol,3*data_cols,NULL,3*data_cols,NULL);CHKERRQ(ierr); 725 /* ierr = MatCreateAIJ(comm, */ 726 /* nloc*bs, nLocalSelected*bs, */ 727 /* PETSC_DETERMINE, PETSC_DETERMINE, */ 728 /* 3*data_cols, NULL, */ 729 /* 3*data_cols, NULL, */ 730 /* &Prol); */ 731 /* CHKERRQ(ierr); */ 732 733 /* can get all points "removed" - but not on geomg */ 734 ierr = MatGetSize(Prol, &kk, &jj);CHKERRQ(ierr); 735 if (jj==0) { 736 ierr = PetscInfo(pc,"ERROE: no selected points on coarse grid\n");CHKERRQ(ierr); 737 ierr = PetscFree(clid_flid);CHKERRQ(ierr); 738 ierr = MatDestroy(&Prol);CHKERRQ(ierr); 739 *a_P_out = NULL; /* out */ 740 PetscFunctionReturn(0); 741 } 742 743 { 744 PetscReal *coords; 745 PetscInt data_stride; 746 PetscInt *crsGID = NULL; 747 Mat Gmat2; 748 749 if (dim != data_cols) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"dim %D != data_cols %D",dim,data_cols); 750 /* grow ghost data for better coarse grid cover of fine grid */ 751 #if defined PETSC_GAMG_USE_LOG 752 ierr = PetscLogEventBegin(petsc_gamg_setup_events[SET5],0,0,0,0);CHKERRQ(ierr); 753 #endif 754 /* messy method, squares graph and gets some data */ 755 ierr = getGIDsOnSquareGraph(nLocalSelected, clid_flid, Gmat, &selected_2, &Gmat2, &crsGID);CHKERRQ(ierr); 756 /* llist is now not valid wrt squared graph, but will work as iterator in 'triangulateAndFormProl' */ 757 #if defined PETSC_GAMG_USE_LOG 758 ierr = PetscLogEventEnd(petsc_gamg_setup_events[SET5],0,0,0,0);CHKERRQ(ierr); 759 #endif 760 /* create global vector of coorindates in 'coords' */ 761 if (size > 1) { 762 ierr = PCGAMGGetDataWithGhosts(Gmat2, dim, pc_gamg->data, &data_stride, &coords);CHKERRQ(ierr); 763 } else { 764 coords = (PetscReal*)pc_gamg->data; 765 data_stride = pc_gamg->data_sz/pc_gamg->data_cell_cols; 766 } 767 ierr = MatDestroy(&Gmat2);CHKERRQ(ierr); 768 769 /* triangulate */ 770 if (dim == 2) { 771 PetscReal metric,tm; 772 #if defined PETSC_GAMG_USE_LOG 773 ierr = PetscLogEventBegin(petsc_gamg_setup_events[SET6],0,0,0,0);CHKERRQ(ierr); 774 #endif 775 ierr = triangulateAndFormProl(selected_2, data_stride, coords,nLocalSelected, clid_flid, agg_lists, crsGID, bs, Prol, &metric);CHKERRQ(ierr); 776 #if defined PETSC_GAMG_USE_LOG 777 ierr = PetscLogEventEnd(petsc_gamg_setup_events[SET6],0,0,0,0);CHKERRQ(ierr); 778 #endif 779 ierr = PetscFree(crsGID);CHKERRQ(ierr); 780 781 /* clean up and create coordinates for coarse grid (output) */ 782 if (size > 1) ierr = PetscFree(coords);CHKERRQ(ierr); 783 784 ierr = MPI_Allreduce(&metric, &tm, 1, MPIU_REAL, MPIU_MAX, comm);CHKERRQ(ierr); 785 if (tm > 1.) { /* needs to be globalized - should not happen */ 786 ierr = PetscInfo1(pc," failed metric for coarse grid %e\n",(double)tm);CHKERRQ(ierr); 787 ierr = MatDestroy(&Prol);CHKERRQ(ierr); 788 } else if (metric > .0) { 789 ierr = PetscInfo1(pc,"worst metric for coarse grid = %e\n",(double)metric);CHKERRQ(ierr); 790 } 791 } else SETERRQ(comm,PETSC_ERR_PLIB,"3D not implemented for 'geo' AMG"); 792 { /* create next coords - output */ 793 PetscReal *crs_crds; 794 ierr = PetscMalloc1(dim*nLocalSelected, &crs_crds);CHKERRQ(ierr); 795 for (kk=0; kk<nLocalSelected; kk++) { /* grab local select nodes to promote - output */ 796 PetscInt lid = clid_flid[kk]; 797 for (jj=0; jj<dim; jj++) crs_crds[jj*nLocalSelected + kk] = pc_gamg->data[jj*nloc + lid]; 798 } 799 800 ierr = PetscFree(pc_gamg->data);CHKERRQ(ierr); 801 pc_gamg->data = crs_crds; /* out */ 802 pc_gamg->data_sz = dim*nLocalSelected; 803 } 804 ierr = ISDestroy(&selected_2);CHKERRQ(ierr); 805 } 806 807 *a_P_out = Prol; /* out */ 808 ierr = PetscFree(clid_flid);CHKERRQ(ierr); 809 ierr = PetscLogEventEnd(PC_GAMGProlongator_GEO,0,0,0,0);CHKERRQ(ierr); 810 PetscFunctionReturn(0); 811 } 812 813 #undef __FUNCT__ 814 #define __FUNCT__ "PCDestroy_GAMG_GEO" 815 static PetscErrorCode PCDestroy_GAMG_GEO(PC pc) 816 { 817 PetscErrorCode ierr; 818 819 PetscFunctionBegin; 820 ierr = PetscObjectComposeFunction((PetscObject)pc,"PCSetCoordinates_C",NULL);CHKERRQ(ierr); 821 PetscFunctionReturn(0); 822 } 823 824 /* -------------------------------------------------------------------------- */ 825 /* 826 PCCreateGAMG_GEO 827 828 Input Parameter: 829 . pc - 830 */ 831 #undef __FUNCT__ 832 #define __FUNCT__ "PCCreateGAMG_GEO" 833 PetscErrorCode PCCreateGAMG_GEO(PC pc) 834 { 835 PetscErrorCode ierr; 836 PC_MG *mg = (PC_MG*)pc->data; 837 PC_GAMG *pc_gamg = (PC_GAMG*)mg->innerctx; 838 839 PetscFunctionBegin; 840 pc_gamg->ops->setfromoptions = PCSetFromOptions_GEO; 841 pc_gamg->ops->destroy = PCDestroy_GAMG_GEO; 842 /* reset does not do anything; setup not virtual */ 843 844 /* set internal function pointers */ 845 pc_gamg->ops->graph = PCGAMGGraph_GEO; 846 pc_gamg->ops->coarsen = PCGAMGCoarsen_GEO; 847 pc_gamg->ops->prolongator = PCGAMGProlongator_GEO; 848 pc_gamg->ops->optprolongator = NULL; 849 pc_gamg->ops->createdefaultdata = PCSetData_GEO; 850 851 ierr = PetscObjectComposeFunction((PetscObject)pc,"PCSetCoordinates_C",PCSetCoordinates_GEO);CHKERRQ(ierr); 852 PetscFunctionReturn(0); 853 } 854